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DNA Structure

2015-10-19T13:57:12Z

140091865:

DNA, or deoxyribonucleic acid, is a complex biological molecule found predominantly within the [[Nucleus|nucleus]] of the cells of all living organisms. There are three different types of DNA- A, B and Z. B form is by far the most abundant at neutral pH. It is the typical right-handed double helix structure found in most organisms. Type A DNA is similar in structure but much thicker than type B and with shorter distances between base pairs. Type Z is completely different to the other two types in the sense that it is a left-handed double helix rather than right-handed. The rest of this page describes the B form of DNA in more detail. 

Each [[Nucleotide|nucleotide]] within the DNA structure is composed of three subunits- a [[Deoxyribose sugar|deoxyribose sugar]], a [[Phosphate group|phosphate]] and one of four organic bases: [[Adenine|adenine]] (A), [[Cytosine|cytosine]] (C), [[Guanine|guanine]] (G) and [[Thymine|thymine]] (T).  Adenine and guanine are derivatives of [[Purines|purine]] and are therefore called purines, whereas cytosine and thymine are derivatives of [[Pyrimidines|pyrimidine]] and hence called pyrimidines <ref>Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition</ref>. All four of these bases are planar <ref>Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition</ref> and can be arranged in any order to create a strand of DNA. Single strands of DNA are almost never seen in natural biology as two strands can join together via hydrogen bonds between specific base pairs to form the more stable right-handed [[Double helix|double helix]] structure. The two strands of DNA in a double helix run anti-parallel to one another. This essentially means they have opposite polarity (one strand runs 5' to 3', whilst the other runs 3' to 5'). The 5' carbon has a phosphate group (PO4 3-) attached to it and the 3' carbon a [[Hydroxyl group|hydroxyl group]] (OH) <ref>Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition</ref>. This is what gives the DNA molecule directionality.

A [[Hydrogen bonds|hydrogen bond]] is a weak electrostatic force of attraction between an [[Electronegativity|electronegative]] atom (e.g. O, N or F) and a hydrogen atom bonded to another electronegative atom. Which bases pair with one another is very specific due to their structures only being able to form hydrogen bonds in certain places. Adenine pairs with thymine by two hydrogen bonds and cytosine pairs with guanine by three hydrogen bonds (Berg et. al, 2011, pp.5). Between the G-C base pairs there are 3 hydrogen bonds which makes this bond pair stronger than the A-T base pair. This third hydrogen bond in G-C base pairs occurs between the additional exocyclic amino group on guanine and the C2 keto group on cytosine <ref>BioWiki, available at:fckLRhttp://biowiki.ucdavis.edu/Genetics/Unit_I%3A_Genes,_Nucleic_Acids,_Genomes_and_Chromosomes/Chapter_2._Structures_of_nucleic_acids/B-Form,_A-Form,_Z-Form_of_DNA fckLRlast accessed 27.11.14</ref>. This explains why G-C rich DNA requires higher temperatures to [[Denature|denature]] it as there is greater bonding between base pairs. The pairing in DNA is highly specific- adenine only pairs with thymine and likewise, guanine only pairs with cytosine. This is because a purine can ony base pair with a pyrimidine (i.e. no purine-purine or pyrimidine-pyrimidine base pairs can occur). This is because the distance is too great for hydrogen bonds to form between two pyrimidines and there is not enough space (the diameter of the helix is just 20 Å <ref>Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition</ref>) for two purines to pair within the helix<ref>DNA tutorial, available at: http://www.dnatutorial.com/BasePairing.shtml last accessed 27.11.14</ref>.  

The phosphate-sugar framework/backbone is on the outside of the molecule so as to protect the organic bases on the inside. The bonds in DNA are phosphodiesterbonds. The bases are almost perpendicular to the framework and each turn of the helix is 3.4 nm <ref>BioWiki, available at:fckLRhttp://biowiki.ucdavis.edu/Genetics/Unit_I%3A_Genes,_Nucleic_Acids,_Genomes_and_Chromosomes/Chapter_2._Structures_of_nucleic_acids/B-Form,_A-Form,_Z-Form_of_DNA fckLRlast accessed 27.11.14</ref>. With there being 10 bases within each turn, each adjacent base is separated by 0.34 nm <ref>Jeremy M. Berg, John L. Tymoczko and Lubert Stryer (2011), Biochemistry, 7th edition</ref>. The phosphate-sugar framework does not however completely contain the bases inside. Each molecule of DNA contains a major and minor groove- the major being deep and broad and the minor being shallow and thin. Proteins bind to the floors of these grooves specifically by hydrogen bonds and [[Van der waals forces|Van der Waals' forces]] <ref>Atlas of Genetics and Cytogenetics in Oncology and Haematology, available at: http://atlasgeneticsoncology.org/Educ/DNAEngID30001ES.html last accessed 27.11.14</ref>. This process is essential for many biological pathways<ref>About Education, available at: http://chemistry.about.com/od/chemistryglossary/g/hbond.htm last accessed 27.11.14</ref>.  

=== References: ===

<references />

SNARE

2014-11-25T16:50:34Z

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= SNARE Proteins =

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) are [[Transmembrane proteins|transmembrane proteins]] that are involved in the catalysis of membrane fusion events within the cell by bringing [[Vesicles|vesicles]] together [[Cell membranes|cell membranes]] and [[Organelle|organelle membranes]]<ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman. (P.378)</ref>. This process allows for efficient transport of substances ( the vesicles' cargo) within vesicles to their correct final location in the cell.

SNAREs are present in organelle membranes and vesicles. There are two types of SNARE protein, v-SNARE ( vesicle SNARE)  and t-SNARE (target membrane SNARE). They exist in complementary pairs of a t-SNARE atttched to the membrane of the target organelle and a v-SNARE on the membrane of the vesicle to be released <ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science (P.G:36)</ref>. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it; in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking.<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science (P.763)</ref>. This means that a specific v-SNARE will only bind to the specific t-SNARE due to its complementary shape therefore the vesicles are not directed to an incorrect location and the cell is able to use the vesicles' cargo in that specific location. <ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman. (P.948)</ref>

== Fusion ==

Once the SNAREs are bound to each other a SNARE complex is formed and the helical domains of the t and v SNAREs wrap around eachother anchoring the vesicle and the [[Plasma membrane|Plasma membrane]] together . The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together to form the four helix bundle to faclitate [[Exocytosis|Exocytosis]]  <ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science (P.763)</ref>. The energy needed to carry out exocytosis is thought to come from the energy freed when the membranes are pulled together and water is squeezed out. Fusion, however is not always an immediate process as it relies on an extracellular signal.<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science (P.763)</ref> 

=== References ===

<references />

SNARE

2014-11-25T16:32:30Z

140091865:

= SNARE Proteins =

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) are [[Transmembrane proteins|transmembrane proteins]] that are involved in the catalysis of membrane fusion events within the cell by bringing [[Vesicles|vesicles]] together [[Cell membranes|cell membranes]] and [[Organelle|organelle membranes]]<ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. This process allows for efficient transport of substances ( the vesicles' cargo) within vesicles to their correct final location in the cell.

SNAREs are present in organelle membranes and vesicles. There are two types of SNARE protein, v-SNARE ( vesicle SNARE)  and t-SNARE (target membrane SNARE). They exist in complementary pairs of a t-SNARE atttched to the membrane of the target organelle and a v-SNARE on the membrane of the vesicle to be released <ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it; in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking.<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. This means that a specific v-SNARE will only bind to the specific t-SNARE due to its complementary shape therefore the vesicles are not directed to an incorrect location and the cell is able to use the vesicles' cargo in that specific location. 

== Fusion ==

Once the SNAREs are bound to each other a SNARE complex is formed and the helical domains of the t and v SNAREs wrap around eachother anchoring the vesicle and the [[Plasma membrane|Plasma membrane]] together . The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together to form the four helix bundle to faclitate [[Exocytosis|Exocytosis]]  <ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. The energy needed to carry out exocytosis is thought to come from the energy freed when the membranes are pulled together and water is squeezed out. Fusion, however is not always an immediate process as it relies on an extracellular signal.<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref> 

=== References ===

<references />

SNARE

2014-11-25T16:11:25Z

140091865:

= SNARE Proteins =

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) are [[Transmembrane proteins|transmembrane proteins]] that are involved in the catalysis of membrane fusion events within the cell by bringing [[Vesicles|vesicles]] together [[Cell_membranes|cell membranes]] and [[Organelle|organelle membranes]]<ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. This process allows for efficient transport of substances ( the vesicles' cargo) within vesicles to their correct final location in the cell.

SNAREs are present in organelle membranes and vesicles. There are two types of SNARE protein, v-SNARE ( vesicle SNARE)  and t-SNARE (target membrane SNARE). They exist in complementary pairs of a t-SNARE atttched to the membrane of the target organelle and a v-SNARE on the membrane of the vesicle to be released<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it; in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking.<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. This means that a specific v-SNARE will only bind to the specific t-SNARE due to its complementary shape therefore the vesicles are not directed to an incorrect location and the cell is able to use the vesicles' cargo in that specific location. 

 Once the SNAREs are bound to each other a SNARE complex is formed and the helical domains of the t and v SNAREs wrap around eachother anchoring the vesicle and the [[Plasma membrane|Plasma membrane]] together . The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together to form the four helix bundle to faclitate [[Exocytosis|Exocytosis]]  <ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. 

=== References ===

<references />

SNARE

2014-11-25T15:39:25Z

140091865:

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) are [[Transmembrane proteins|transmembrane proteins]] that are involved in the catalysis of membrane fusion events within the cell by bringing together cell membranes and organelle membranes<ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. This process allows for efficient transport of substances within membrane vesicles to their correct final location in the cell.

SNAREs are present in organelle membranes and vesicles, there ar two types of SNARE protein, v-SNARE ( vesicle SNARE)  and t-SNARE (target membrane SNARE). They exist in complementary pairs of a t-SNARE atttched to the membrane of the target organelle and a v-SNARE on the membrane of the vesicle to be released<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it; in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. Once the SNAREs are bound to each other a SNARE complex is formed in which the helical domains of the t and v SNAREs anchor the vesicle and the [[Plasma membrane|Plasma membrane]] together. The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together to form the four helix bundle to faclitate [[Exocytosis|Exocytosis]]  <ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. 

 

=== References ===

<references />

SNARE

2014-11-25T15:38:55Z

140091865:

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) are [[Transmembrane proteins|transmembrane proteins]] that are involved in the catalysis of membrane fusion events within the cell by bringing together cell membranes and organelle membranes<ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. This process allows for efficient transport of substances within membrane vesicles to their correct final location in the cell.

SNAREs are present in organelle membranes and vesicles, there ar two types of SNARE protein, v-SNARE ( vesicle SNARE)  and t-SNARE (target membrane SNARE). They exist in complementary pairs of a t-SNARE atttched to the membrane of the target organelle and a v-SNARE on the membrane of the vesicle to be released<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it; in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. Once the SNAREs are bound to each other a SNARE complex is formed in which the helical domains of the t and v SNAREs anchor the vesicle and the [[Plasma membrane|Plasma membrane]] together. The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together to form the four helix bundle to faclitate [[Exocytosis|Exocytosis<ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>]]. 

 

=== References ===

<references />

SNARE

2014-11-25T15:38:26Z

140091865:

SNARE

2014-11-25T15:37:24Z

140091865:

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) are [[Transmembrane proteins|transmembrane proteins]] that are involved in the catalysis of membrane fusion events within the cell by bringing together cell membranes and organelle membranes<ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. This process allows for efficient transport of substances within membrane vesicles to their correct final location in the cell.

SNAREs are present in organelle membranes and vesicles, there ar two types of SNARE protein, v-SNARE ( vesicle SNARE)  and t-SNARE (target membrane SNARE). They exist in complementary pairs of a t-SNARE atttched to the membrane of the target organelle and a v-SNARE on the membrane of the vesicle to be released<ref>Alberts B., Johnson A., Lewis J., Raff M., Roberts K., Walter P. (2008) Molecular Biology of The Cell, 5th Edition New York: Garland Science</ref>. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it; in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking. Once the SNAREs are bound to each other a SNARE complex is formed in which the helical domains of the t and v SNAREs anchor the vesicle and the [[Plasma membrane|Plasma membrane]] together. The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together to form the four helix bundle to faclitate [[Exocytosis]] 

 

=== References ===

<references />

SNARE

2014-11-25T15:29:58Z

140091865:

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) are [[Transmembrane proteins|transmembrane proteins]] that are involved in the catalysis of membrane fusion events within the cell by bringing together cell membranes and organelle membranes<ref>Berg J., Tymoczko J and Stryer L. (2012) Biochemistry, 7th edition, New York: WH Freeman.</ref>. This process allows for efficient transport of substances within membrane vesicles to their correct final location in the cell.

SNAREs are present in organelle membranes and vesicles ad there ar two types of SNARE protein, v-SNARE ( vesicle SNARE)  and t-SNARE (target membrane SNARE). They exist in complementary pairs of a t-SNARE atttched to the membrane of the target organelle and a v-SNARE on the membrane of the vesicle to be released. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it and in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking. Once the SNAREs are bound to each other a SNARE complex is formed in which the helical domains of the t and v SNAREs anchor the vesicle and the [[Plasma membrane|Plasma membrane]] together. The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together to form the four helix bundle to faclitate [[Exocytosis]] 

 

=== References ===

<references />

SNARE

2014-11-25T14:41:26Z

140091865:

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) are [[Transmembrane_proteins|transmembrane proteins]] that are involved in the catalysis of membrane fusion events within the cell by bringing together cell membranes and organelle membranes. This process allows for efficient transport of substances within membrane vesicles to their correct final location in the cell.

SNAREs are present in organelle membranes and vesicles ad there ar two types of SNARE protein, v-SNARE ( vesicle SNARE)  and t-SNARE (target membrane SNARE). They exist in complementary pairs of a t-SNARE atttched to the membrane of the target organelle and a v-SNARE on the membrane of the vesicle to be released. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it and in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking. Once the SNAREs are bound to each other a SNARE complex is formed in which the helical domains of the t and v SNAREs anchor the vesicle and the [[Plasma_membrane|Plasma membrane]] together. The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together to form the four helix bundle to faclitate [[Endocytosis]]. 

=== References ===

<references />

SNARE

2014-11-25T14:28:32Z

140091865:

SNAREs are transmembrane [[Proteins|proteins]] involved in catalysing membrane fusion events in cells. There are two types of SNARE protein, [[V-SNARE|v-SNARE]] and [[T-SNARE|t-SNARE]]. The v-SNARE is attatched to the membrane of the vesicle to be released. The t-SNARE is integrated into the target [[Organelles|organelles]] [[Membrane|membrane]]. The v-SNARE's have complimentary shaped t-SNAREs which they bind to.

SNARE proteins (Soluble N-ethymaleimide- sensitive –factor attachment proteins) catalyse membrane fusion events within the cell by bringing together cell membranes and organelle membranes. This process allows for efficient transport of substances within membrane vesicles. SNAREs are present in organelle membranes and vesicles. They exist in complementary pairs of a t-SNARE (target membrane SNARE) on the membrane and a v-SNARE ( ) on the vesicle. The specific v-SNARE on the vesicle recognises the correct t-SNARE and binds to it and in doing so the vesicle is directed to its correct location in the cell. SNARES provide an “extra layer of specificity” to ensure efficient intracellular trafficking. Once the SNAREs are bound to each other a SNARE complex is formed in which the helical domains of the t and v SNAREs anchor the vesicle and the plasma membrane together. The v-SNARE consists of just one protein where as the t-SNARE consists of two or three and it is these proteins which bind together forming the four helix bundle.